Ideally, and in practice, are not the same thing here... People downvote things they disagree with, including unconventional views, all the time.
It's quite possible for the majority of people to vote based on agreement, and yet have the overall score of the comment be determined by those who vote by quality. Of the ones who vote by agreement, some will agree and some will disagree, and they end up cancelling each other out. The remaining comment score is made up of those who voted because it was a well-reasoned argument.
Reddit has the "Controversial" tab for this, though HN unfortunately doesn't make a distinction between a comment with 50 upvotes and 40 downvotes vs. one with 10 upvotes and 0 downvotes.
It's possible for this to happen, but I don't think there are that many hot-button issues where the two sides are exactly balanced. More commonly there will be at least a slight skew in one direction or another, which gets magnified in absolute score the more people there are who vote based on agreement. For example, if there's a 60/40 opinion skew among people who vote based on agreement on a particular topic, and 20 people vote that way, you already have an 8-point rating gap between the popular and unpopular comments (+12/-8 versus +8/-12). On really high-traffic topics, where 100 people might up/downvote based on agreement, you only need a tiny skew from 50/50 for the votes to pile up in one direction or another.
I think in practice that often swamps the quality-based voting, especially on high-traffic articles: you sometimes see extremely short and not particularly insightful comments that express a popular sentiment up at +40 or more.
Certainly, some people stop, think, disagree, and downvote. I believe that this is the case when the original comment is sloppy, and generally warrants a reply. In some cases, especially various kinds of politics, the replies are omitted presumably because of fatigue. Such people have already replied to the argument enough times in their life to not want to do it again. That could be interpreted as a failure of domain research on the part of the original commenter, but I don't like to blame people for not being "well-read".
up-promote vs. down-demote: affecting order-of-presentation and karma
left-agree vs. right-disagress: a mini-poll per comment, with no censorious effect on presentation or numerical-reputational effect on karma